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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $species_info = array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ) $local_species = 'atr' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $species_info = array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ) $local_species = 'atr' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ), 'gf_id' => 'HOM05D001295', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001295' ), 'data_identifier' => 'HOM05D001295', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001295', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24250' => 'bna', 'A04p02120' => 'bna', 'A04p32720' => 'bna', 'A05p03770' => 'bna', 'A05p43870' => 'bna', 'A07p24710' => 'bna', 'A09p42860' => 'bna', 'A09p51820' => 'bna', 'Aa31LG10G13880' => 'aar', 'Aa31LG1G25190' => 'aar', 'Aa31LG1G25200' => 'aar', 'Aa31LG5G13780' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2491' => 'aag', 'Actinidia11291' => 'ach', 'Actinidia26500' => 'ach', 'Actinidia27088' => 'ach', 'Actinidia34573' => 'ach', 'Actinidia34578' => 'ach', 'AL3G12950' => 'aly', 'AL3G52180' => 'aly', 'AL4G36180' => 'aly', 'AL4G42190' => 'aly', 'AL4G42200' => 'aly', 'AL5G41470' => 'aly', 'Aqoxy2G04125' => 'aox', 'Aqoxy5G00029' => 'aox', 'Aqoxy5G00377' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HI5HP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NSI0A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.982DXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9S43MM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1V79H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CA0DYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IT1C9S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4PJLA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YST1YA' => 'arhy', 'AT2G43460' => 'ath', 'AT2G43465' => 'ath', 'AT3G03320' => 'ath', 'AT3G59540' => 'ath', 'ATR0743G262' => 'atr', 'Atru.chr11.1085' => 'acertr', 'Atru.chr11.1086' => 'acertr', 'Atru.chr2.3464' => 'acertr', 'Atru.chr2.3465' => 'acertr', 'Atru.chr2.3478' => 'acertr', 'Atru.chr2.3479' => 'acertr', 'Atru.chr4.1272' => 'acertr', 'Atru.chr4.2286' => 'acertr', 'Atru.chr7.1201' => 'acertr', 'AUR62000282' => 'cqu', 'AUR62002354' => 'cqu', 'AUR62002356' => 'cqu', 'AUR62006630' => 'cqu', 'AUR62023829' => 'cqu', 'BcaB01g03382' => 'bca', 'BcaB02g07458' => 'bca', 'BcaB02g08216' => 'bca', 'BcaB02g08938' => 'bca', 'BcaC01g05233' => 'bca', 'BcaC02g07177' => 'bca', 'BcaC02g07178' => 'bca', 'BcaC02g10060' => 'bca', 'BcaC02g12392' => 'bca', 'BcaC05g30303' => 'bca', 'BcaC07g40486' => 'bca', 'BcaC08g44995' => 'bca', 'BolC2t06464H' => 'bol', 'BolC3t15248H' => 'bol', 'BolC4t22080H' => 'bol', 'BolC4t24899H' => 'bol', 'BolC4t28547H' => 'bol', 'BolC5t35010H' => 'bol', 'BolC6t37788H' => 'bol', 'BolC8t51056H' => 'bol', 'BolC9t54939H' => 'bol', 'BraA03t11634Z' => 'bra', 'BraA04t15938Z' => 'bra', 'BraA04t18736Z' => 'bra', 'BraA05t19364Z' => 'bra', 'BraA05t19365Z' => 'bra', 'BraA05t23124Z' => 'bra', 'BraA07t30115Z' => 'bra', 'BraA09t40617Z' => 'bra', 'C01p44730' => 'bna', 'C03p28920' => 'bna', 'C04p04470' => 'bna', 'C04p33370' => 'bna', 'C04p70430' => 'bna', 'C05p63460' => 'bna', 'C06p26250' => 'bna', 'CAN.G321.34' => 'can', 'CAN.G65.159' => 'can', 'CANSAT35G1007' => 'cansat', 'CANSAT54G0654' => 'cansat', 'CARHR077360' => 'chi', 'CARHR138530' => 'chi', 'CARHR138550' => 'chi', 'CARHR169940' => 'chi', 'Carub.0003s0249' => 'cru', 'Carub.0004s2591' => 'cru', 'Carub.0004s2592' => 'cru', 'Carub.0005s2628' => 'cru', 'Ca_01246_v3' => 'car', 'Ca_18159_v3' => 'car', 'Ca_20804_v3' => 'car', 'CBR_g21778' => 'cbr', 'CBR_g39257' => 'cbr', 'CBR_g50796' => 'cbr', 'Cc03_g12290' => 'ccan', 'Cc07_g18950' => 'ccan', 'Cc09_g04990' => 'ccan', 'CDE02G2807' => 'cde', 'CDE04G3365' => 'cde', 'CDE07G1170' => 'cde', 'CDE09G0242' => 'cde', 'Cfa015203' => 'cfa', 'Ciclev10013279m.g' => 'ccl', 'Ciclev10021418m.g' => 'ccl', 'Ciclev10021666m.g' => 'ccl', 'Ciclev10023214m.g' => 'ccl', 'CiPaw.01G095500' => 'cil', 'CiPaw.05G016100' => 'cil', 'CiPaw.07G083100' => 'cil', 'CiPaw.07G083200' => 'cil', 'CiPaw.08G112800' => 'cil', 'ClCG06G000980' => 'cla', 'ClCG06G000990' => 'cla', 'ClCG06G001010' => 'cla', 'ClCG07G011710' => 'cla', 'COL.COLO4_08217' => 'col', 'COL.COLO4_09274' => 'col', 'COL.COLO4_21796' => 'col', 'COL.COLO4_34336' => 'col', 'Cpa.g.sc9.322' => 'cpa', 'Cpa.g.sc9.324' => 'cpa', 'Cre07.g325746' => 'cre', 'Cre16.g668650' => 'cre', 'CsaV3_2G010500' => 'csa', 'CsaV3_2G033010' => 'csa', 'CsaV3_4G002500' => 'csa', 'CsaV3_6G006830' => 'csa', 'CsaV3_7G021070' => 'csa', 'CSS0006680' => 'camsi', 'CSS0013705' => 'camsi', 'CSS0015814' => 'camsi', 'CSS0039667' => 'camsi', 'CSS0045865' => 'camsi', 'DCAR_024440' => 'dca', 'DCAR_026527' => 'dca', 'DCAR_028425' => 'dca', 'Dinv05085' => 'din', 'Dinv05087' => 'din', 'Dinv21361' => 'din', 'Dinv29080' => 'din', 'Dinv44160' => 'din', 'Duzib151G0048' => 'dzi', 'Duzib212G0002' => 'dzi', 'Duzib212G0222' => 'dzi', 'Duzib268G1657' => 'dzi', 'ECA240G0894' => 'eca', 'ECA240G1882' => 'eca', 'EL10Ac3g06016' => 'bvu', 'EL10Ac3g06017' => 'bvu', 'EL10Ac3g06020' => 'bvu', 'EL10Ac4g10012' => 'bvu', 'EL10Ac6g13768' => 'bvu', 'Eucgr.H00340' => 'egr', 'Eucgr.K00006' => 'egr', 'FAN09G3849' => 'fan', 'FAN14G2811' => 'fan', 'FAN15G1214' => 'fan', 'FAN15G2624' => 'fan', 'FAN20G0399' => 'fan', 'FAN24G0013' => 'fan', 'FAN24G0827' => 'fan', 'FAN27G0739' => 'fan', 'FAN27G1301' => 'fan', 'FvH4_2g11140' => 'fve', 'FvH4_2g12030' => 'fve', 'FvH4_2g24830' => 'fve', 'FvH4_3g31637' => 'fve', 'FvH4_6g00180' => 'fve', 'Glyma.05G143700' => 'gma', 'Glyma.08G100000' => 'gma', 'Glyma.13G221500' => 'gma', 'Glyma.13G345600' => 'gma', 'Glyma.13G345802' => 'gma', 'Glyma.15G028500' => 'gma', 'Glyma.15G028700' => 'gma', 'Glyma.15G090800' => 'gma', 'Gohir.A02G010900' => 'ghi', 'Gohir.A02G093300' => 'ghi', 'Gohir.A02G093600' => 'ghi', 'Gohir.A05G348100' => 'ghi', 'Gohir.A05G360950' => 'ghi', 'Gohir.A08G092500' => 'ghi', 'Gohir.A09G212400' => 'ghi', 'Gohir.A10G139800' => 'ghi', 'Gohir.D02G011500' => 'ghi', 'Gohir.D02G111400' => 'ghi', 'Gohir.D02G111500' => 'ghi', 'Gohir.D04G111150' => 'ghi', 'Gohir.D08G098300' => 'ghi', 'Gohir.D08G125866' => 'ghi', 'Gohir.D08G205200' => 'ghi', 'Gohir.D09G205900' => 'ghi', 'Gohir.D10G127000' => 'ghi', 'Gohir.D11G131701' => 'ghi', 'Gorai.003G121300' => 'gra', 'Gorai.004G105900' => 'gra', 'Gorai.005G014500' => 'gra', 'Gorai.005G126300' => 'gra', 'Gorai.005G126400' => 'gra', 'Gorai.006G229800' => 'gra', 'Gorai.011G140000' => 'gra', 'GSVIVG01004102001' => 'vvi', 'GSVIVG01010854001' => 'vvi', 'GSVIVG01019051001' => 'vvi', 'HanXRQChr06g0173351' => 'han', 'HanXRQChr13g0419451' => 'han', 'HanXRQChr17g0536331' => 'han', 'Haze_01445' => 'cav', 'Haze_01447' => 'cav', 'Haze_02607' => 'cav', 'Haze_02612' => 'cav', 'Haze_10244' => 'cav', 'Haze_27776' => 'cav', 'Hma1.2p1_0022F.1_g014786' => 'hma', 'Hma1.2p1_0095F.1_g047580' => 'hma', 'Hma1.2p1_0113F.1_g055140' => 'hma', 'Hma1.2p1_0401F.1_g144800' => 'hma', 'Hma1.2p1_0487F.1_g163630' => 'hma', 'Hma1.2p1_3259F.1_g334640' => 'hma', 'Hma1.2p1_3259F.1_g334643' => 'hma', 'HPP92_007597' => 'vpl', 'HPP92_007599' => 'vpl', 'HPP92_023719' => 'vpl', 'Hund03182' => 'sun', 'Hund07369' => 'sun', 'Hund12401' => 'sun', 'Hund21918' => 'sun', 'Lalb_Chr01g0003071' => 'lal', 'Lalb_Chr03g0026001' => 'lal', 'Lalb_Chr13g0294031' => 'lal', 'Lalb_Chr14g0372541' => 'lal', 'Lalb_Chr14g0372561' => 'lal', 'Lalb_Chr14g0372571' => 'lal', 'Lalb_Chr15g0086641' => 'lal', 'Lalb_Chr18g0055141' => 'lal', 'Lalb_Chr19g0138401' => 'lal', 'Lalb_Chr22g0352051' => 'lal', 'Lalb_Chr24g0396731' => 'lal', 'Lj3A83T16' => 'lonja', 'Lj3C135G1' => 'lonja', 'Lj3g0012540' => 'lja', 'Lj3g0015879' => 'lja', 'Lj3g0016601' => 'lja', 'Lj3g0020600' => 'lja', 'Lj6g0026341' => 'lja', 'Lsat_1_v5_gn_3_110661' => 'lsa', 'Lsat_1_v5_gn_3_22520' => 'lsa', 'Manes.04G047700' => 'mes', 'Manes.11G125700' => 'mes', 'Manes.11G126000' => 'mes', 'Manes.12G002500' => 'mes', 'Manes.13G002900' => 'mes', 'Mapoly0009s0137' => 'mpo', 'Mapoly0209s0009' => 'mpo', 'MBI01_g38808_MAGBIO' => 'mbi', 'MBI05_g05676_MAGBIO' => 'mbi', 'MBI07_g18527_MAGBIO' => 'mbi', 'MBI12_g18648_MAGBIO' => 'mbi', 'MBI14_g39538_MAGBIO' => 'mbi', 'MBI16_g34949_MAGBIO' => 'mbi', 'MBI17_g23522_MAGBIO' => 'mbi', 'MCO02G190' => 'mco', 'MD03G1210200' => 'mdo', 'MD04G1045900' => 'mdo', 'MD04G1046100' => 'mdo', 'MD04G1247500' => 'mdo', 'MD05G1254000' => 'mdo', 'MD05G1339000' => 'mdo', 'MD06G1106700' => 'mdo', 'MD11G1200200' => 'mdo', 'MD12G1262900' => 'mdo', 'MD13G1258200' => 'mdo', 'MD14G1129300' => 'mdo', 'MD15G1353900' => 'mdo', 'MD16G1190800' => 'mdo', 'Medtr2g018680' => 'mtr', 'Medtr2g027210' => 'mtr', 'Medtr2g099125' => 'mtr', 'Medtr2g099135' => 'mtr', 'Medtr4g068040' => 'mtr', 'Medtr8g079485' => 'mtr', 'MELO3C001160.2' => 'cme', 'MELO3C008569.2' => 'cme', 'MELO3C022439.2' => 'cme', 'MELO3C022441.2' => 'cme', 'Migut.F01852' => 'egut', 'Migut.G01305' => 'egut', 'Migut.G01307' => 'egut', 'Migut.G01308' => 'egut', 'Migut.G01326' => 'egut', 'Migut.G01331' => 'egut', 'Migut.N03094' => 'egut', 'MSTRG.22012' => 'ama', 'MSTRG.4291' => 'ama', 'Nitab4.5_0000751g0080' => 'nta', 'Nitab4.5_0000819g0050' => 'nta', 'Nitab4.5_0001586g0250' => 'nta', 'Nitab4.5_0002143g0010' => 'nta', 'Nitab4.5_0002553g0060' => 'nta', 'Nitab4.5_0004325g0050' => 'nta', 'Nitab4.5_0005221g0040' => 'nta', 'Nitab4.5_0006561g0010' => 'nta', 'Nitab4.5_0007609g0010' => 'nta', 'Nitab4.5_0011792g0020' => 'nta', 'Nitab4.5_0013215g0010' => 'nta', 'Nitab4.5_0016488g0010' => 'nta', 'Nitab4.5_0021847g0010' => 'nta', 'Nn1g09559' => 'nnu', 'Nn1g09570' => 'nnu', 'Nn7g37575' => 'nnu', 'Oeu015632.1' => 'oeu', 'Oeu020777.1' => 'oeu', 'Oeu022684.1' => 'oeu', 'Oeu027749.1' => 'oeu', 'Oeu034441.1' => 'oeu', 'Oeu056129.3' => 'oeu', 'Os07g0546700' => 'osa', 'Os08g0541950' => 'osa', 'Os11g0265500' => 'osa', 'Os11g0433900' => 'osa', 'Peaxi162Scf00180g00045' => 'pax', 'Peaxi162Scf00253g00512' => 'pax', 'Peaxi162Scf00296g00811' => 'pax', 'Peaxi162Scf00627g00008' => 'pax', 'PGR042G0464' => 'pgr', 'PGR042G1325' => 'pgr', 'PGR083G0712' => 'pgr', 'PGR142G1205' => 'pgr', 'PGR142G2463' => 'pgr', 'PGSC0003DMG400007429' => 'stu', 'PGSC0003DMG400016814' => 'stu', 'PGSC0003DMG400026920' => 'stu', 'Phvul.002G177700' => 'pvu', 'Phvul.005G154400' => 'pvu', 'Phvul.005G154600' => 'pvu', 'Phvul.006G168118' => 'pvu', 'Potri.007G131800' => 'ptr', 'Potri.007G132100' => 'ptr', 'Potri.008G076100' => 'ptr', 'Potri.010G181200' => 'ptr', 'Potri.017G026000' => 'ptr', 'Pp3c10_20240' => 'ppa', 'Pp3c12_17990' => 'ppa', 'Pp3c13_1370' => 'ppa', 'Pp3c18_13860' => 'ppa', 'Pp3c3_25640' => 'ppa', 'Pp3c4_11700' => 'ppa', 'PRCOL_00004758' => 'pco', 'Prupe.1G193400' => 'ppe', 'Prupe.1G198900' => 'ppe', 'Prupe.1G199500' => 'ppe', 'Prupe.1G237900' => 'ppe', 'Prupe.6G363900' => 'ppe', 'Prupe.7G035900' => 'ppe', 'Psat1g192040' => 'psa', 'Psat5g290520' => 'psa', 'Psat7g209440' => 'psa', 'PSO017G1243' => 'pso', 'PSO017G5265' => 'pso', 'PSO210G0430' => 'pso', 'PSO675G4063' => 'pso', 'PSO832G3760' => 'pso', 'PSO837G0039' => 'pso', 'QL01p028728' => 'qlo', 'QL09p019105' => 'qlo', 'QL10p051285' => 'qlo', 'QL10p051312' => 'qlo', 'QL10p051666' => 'qlo', 'QL11p031711' => 'qlo', 'RcHm_v2.0_Chr3g0447551' => 'rch', 'RcHm_v2.0_Chr6g0269441' => 'rch', 'RcHm_v2.0_Chr6g0292651' => 'rch', 'Rhsim02G0082600' => 'rsi', 'Rhsim09G0020700' => 'rsi', 'Rhsim09G0021500' => 'rsi', 'RhsimUnG0137700' => 'rsi', 'RhsimUnG0137800' => 'rsi', 'Sabra07G0107000' => 'sbr', 'Sabra07G0107200' => 'sbr', 'Sabra07G0107500' => 'sbr', 'Sabra07G0118900' => 'sbr', 'Sabra07G0119100' => 'sbr', 'Sabra07G0119200' => 'sbr', 'Sabra07G0119300' => 'sbr', 'Sabra10G0139000' => 'sbr', 'Sabra17G0000100' => 'sbr', 'Sabra17G0000500' => 'sbr', 'Sabra17G0001500' => 'sbr', 'Sabra17G0001700' => 'sbr', 'Sabra17G0015000' => 'sbr', 'Sabra17G0015200' => 'sbr', 'SalBow1G1847' => 'sbo', 'SalBow1G5643' => 'sbo', 'SalBow2G2460' => 'sbo', 'SalBow3G3855' => 'sbo', 'SalBow3G4234' => 'sbo', 'SalBow4G2818' => 'sbo', 'SalBow5G4879' => 'sbo', 'SalBow6G3713' => 'sbo', 'SalBow6G4904' => 'sbo', 'SalBow8G1821' => 'sbo', 'SalBow8G2942' => 'sbo', 'SalBow8G3210' => 'sbo', 'SalBow8G5303' => 'sbo', 'Sc06g0004970' => 'sci', 'Sc16g0010540' => 'sci', 'Sc21g0002910' => 'sci', 'Sed0000422' => 'sed', 'Sed0001553' => 'sed', 'Sed0002070' => 'sed', 'Sed0017723' => 'sed', 'Sed0021210' => 'sed', 'SEGI_20516' => 'sgi', 'SEGI_37645' => 'sgi', 'SGA_v2.0_scaffold12G06175' => 'sas', 'SGA_v2.0_scaffold17G08165' => 'sas', 'SHI14365' => 'shi', 'SMO337G0100' => 'smo', 'SMO367G0857' => 'smo', 'Solyc05g055640.4' => 'sly', 'Solyc06g073130.4' => 'sly', 'Solyc11g008510.3' => 'sly', 'Sopen05g034080' => 'spe', 'Sopen06g029480' => 'spe', 'Sopen11g004300' => 'spe', 'Sp3g02350' => 'spa', 'Sp4g25540' => 'spa', 'Sp4g25550' => 'spa', 'Sp5g03600' => 'spa', 'TAR365G0765' => 'tar', 'TAR633G1947' => 'tar', 'TAR636G3281' => 'tar', 'THA.LOC104803831' => 'tha', 'THA.LOC104803837' => 'tha', 'THA.LOC104805270' => 'tha', 'THA.LOC104816303' => 'tha', 'THA.LOC104820845' => 'tha', 'THA.LOC109116186' => 'tha', 'THA.LOC109116538' => 'tha', 'Thecc.04G173200' => 'tca', 'Thecc.04G173300' => 'tca', 'Thecc.04G174000' => 'tca', 'Thhalv10001710m.g' => 'esa', 'Thhalv10001762m.g' => 'esa', 'Thhalv10006355m.g' => 'esa', 'Thhalv10021391m.g' => 'esa', 'TPR.G26251' => 'tpr', 'TPR.G34195' => 'tpr', 'TPR.G39345' => 'tpr', 'TPR.G6512' => 'tpr', 'TWI15G0029' => 'twi', 'TWI15G0408' => 'twi', 'TWI18G1377' => 'twi', 'TWI36G0068' => 'twi', 'TWI53G2097' => 'twi', 'TWI60G0022' => 'twi', 'TWI77G0945' => 'twi', 'unitig_18.g30056' => 'ugi', 'unitig_37.g12026' => 'ugi', 'unitig_578.g16254' => 'ugi', 'vmacro00675' => 'vma', 'vmacro00676' => 'vma', 'vmacro00677' => 'vma', 'VMungo0251G2801' => 'vmu', 'VMungo1080G0958' => 'vmu', 'Zm00001eb037310' => 'zma', 'Zm00001eb064040' => 'zma', 'Zm00001eb106530' => 'zma', 'Zm00001eb198420' => 'zma' ) $gf_id = 'HOM05D001295' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001295' ) $data_identifier = 'HOM05D001295' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 9, 'cqu' => (int) 5, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 1, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 2, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 13, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 2, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 14, 'sbo' => (int) 13, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb198420' $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